[phenixbb] shaking a PDB without introducing clashes

Nathaniel Echols NEchols at lbl.gov
Sun Mar 28 17:25:46 PDT 2010

On Mar 28, 2010, at 5:17 PM, Francois Berenger wrote:
> I recently used "phenix.pdbtools modify.sites.shake=..."
> in order to have some data from 0.1 to 5A. away from
> the true structure in order to test some scripts.
> I think this introduced clashes in the "shaken" PDBs
> I got.
> Is there a tool/way to avoid this?

I would recommend running geometry regularization on the shaken model:

phenix.pdbtools model.pdb --geometry_regularization


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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